Phage communities in household-related biofilms correlate with bacterial hosts DOI Creative Commons
Stefanie Huttelmaier, Weitao Shuai, Jack T. Sumner

et al.

Frontiers in Microbiomes, Journal Year: 2024, Volume and Issue: 3

Published: Oct. 9, 2024

The average American spends 93% of their time in built environments, almost 70% that is place residence. Human health and well-being are intrinsically tied to the quality our personal environments microbiomes populate them. Conversely, environment microbiome seeded, formed, re-shaped by occupant behavior, cleaning, hygiene food choices, as well geographic location variability infrastructure. Here, we focus on presence viruses household biofilms, specifically showerheads toothbrushes. Bacteriophage, infect bacteria with high host specificity, have been shown drive microbial community structure function through infection horizontal gene transfer environmental systems. Due dynamic environment, extreme temperature changes, periods wetting/drying exposure hygiene/cleaning products, addition low biomass transient nature indoor microbiomes, hypothesize phage these unique different from biofilm interactions. We approach hypothesis using metagenomics, querying 34 toothbrush 92 showerhead metagenomes. Representative biofilms interfaces demonstrate distinct levels interaction. identified 22 complete, 232 quality, 362 medium viral OTUs. Viral richness correlated bacterial but not Shannon or Simpson indices. Of OTUs sufficient coverage (614), 532 were connected 32 families, which only Sphingomonadaceae, Burkholderiaceae, Caulobacteraceae found both toothbrushes showerheads. Low nucleotide identity reference sequences a proportion open reading frames annotated hypothetical unknown indicate harbor many novel uncharacterized phage. results this study reveal paucity information available bacteriophage need for more virus-focused methods DNA extraction specific sequencing aimed at understanding impact environment.

Language: Английский

Response of Soil Phage Communities and Prokaryote–Phage Interactions to Long-Term Drought DOI
Cong Liu, Zhijie Chen, Xinlei Wang

et al.

Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Soil moisture is a fundamental factor affecting terrestrial ecosystem functions. In this study, microscopic enumeration and joint metaviromic metagenomic sequencing were employed together to investigate the impact of prolonged drought on soil phage communities their interactions with prokaryotes in subtropical evergreen forest. Our findings revealed marked reduction abundances prokaryotic viral-like particles, by 73.1% 75.2%, respectively, significantly altered structure under drought. Meanwhile, substantially increased fraction containing lysogenic phages 163%, as well proportion temperate phages. Nonetheless, likely amplified negative prokaryote-phage given nearly doubled links co-occurrence network, higher frequency diversity antiphage defense systems found genomes. Under drought, exerted greater top-down control typical k-strategists including Acidobacteria Chloroflexi. Moreover, phage-encoded auxiliary metabolic genes may host metabolism biosynthesis-related Collectively, study underscore profound interactions. These results also emphasize importance managing levels during amendment microbiome manipulation account for influence

Language: Английский

Citations

0
Targeted viromes and total metagenomes capture distinct components of bee gut phage communities DOI Creative Commons
Dino Lorenzo Sbardellati, Rachel L. Vannette

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: Aug. 23, 2024

Abstract Background Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying phage is lack consensus methods for sampling communities. Here, we compare paired total metagenomes and viral size fraction (viromes) as investigating dsDNA communities associated with GI tract two bee species: European honey Apis mellifera eastern bumble Bombus impatiens . Results We find that viromes successfully enriched phage, thereby increasing recovery, but only in bees. In contrast, bees, recovered greater diversity. Across both species, better sampled low occupancy while were biased towards temperate phage. Additionally, many captured by absent altogether from viromes. Comparing between show commercially reared bees are significantly reduced diversity compared likely reflecting differences bacterial titer a broader context, these results highlight complementary nature targeted viromes, especially when applied environments. Conclusions Overall, suggest studies interested assessing should consider using approaches. However, given constraints virome sampling, may serve sample understanding they will preferentially dominant

Language: Английский

Citations

2
Targeted Viromes and Total Metagenomes Capture Distinct Components of Bee Gut Phage Communities DOI Open Access
Dino Lorenzo Sbardellati, Rachel L. Vannette

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 12, 2024

Abstract Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying phage is lack consensus methods for sampling communities. Here, we compare paired total metagenomes and viral size fraction (viromes) as investigating dsDNA communities associated with GI tract two bee species: European honey Apis mellifera eastern bumble Bombus impatiens . We find that viromes successfully enriched phage, thereby increasing recovery, but only in bees. In contrast, bees, recovered greater diversity. Across both species, better sampled low abundance occupancy while were biased towards temperate prominent phage. Additionally, many captured by absent altogether from viromes. Comparing between show commercially reared bees are significantly reduced diversity compared likely reflecting differences bacterial titer a broader context, these results highlight complementary nature targeted viromes, especially when applied environments. Overall, suggest studies interested assessing should consider using approaches. However, given constraints virome sampling, may serve sample understanding they will preferentially dominant

Language: Английский

Citations

0
Phage communities in household-related biofilms correlate with bacterial hosts DOI Creative Commons
Stefanie Huttelmaier, Weitao Shuai, Jack T. Sumner

et al.

Frontiers in Microbiomes, Journal Year: 2024, Volume and Issue: 3

Published: Oct. 9, 2024

The average American spends 93% of their time in built environments, almost 70% that is place residence. Human health and well-being are intrinsically tied to the quality our personal environments microbiomes populate them. Conversely, environment microbiome seeded, formed, re-shaped by occupant behavior, cleaning, hygiene food choices, as well geographic location variability infrastructure. Here, we focus on presence viruses household biofilms, specifically showerheads toothbrushes. Bacteriophage, infect bacteria with high host specificity, have been shown drive microbial community structure function through infection horizontal gene transfer environmental systems. Due dynamic environment, extreme temperature changes, periods wetting/drying exposure hygiene/cleaning products, addition low biomass transient nature indoor microbiomes, hypothesize phage these unique different from biofilm interactions. We approach hypothesis using metagenomics, querying 34 toothbrush 92 showerhead metagenomes. Representative biofilms interfaces demonstrate distinct levels interaction. identified 22 complete, 232 quality, 362 medium viral OTUs. Viral richness correlated bacterial but not Shannon or Simpson indices. Of OTUs sufficient coverage (614), 532 were connected 32 families, which only Sphingomonadaceae, Burkholderiaceae, Caulobacteraceae found both toothbrushes showerheads. Low nucleotide identity reference sequences a proportion open reading frames annotated hypothetical unknown indicate harbor many novel uncharacterized phage. results this study reveal paucity information available bacteriophage need for more virus-focused methods DNA extraction specific sequencing aimed at understanding impact environment.

Language: Английский

Citations

0